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rstudio / rsconnect

Publish Shiny Applications, RMarkdown Documents, Jupyter Notebooks, Plumber APIs, and more
http://rstudio.github.io/rsconnect/
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rsconnect::deployApp() in R 3.6.1 is not working with an app with Bioconductor dependencies that used to work with R 3.4.3 #384

Closed lcolladotor closed 5 years ago

lcolladotor commented 5 years ago

Hi,

Months ago (over a year ago) I deployed https://jhubiostatistics.shinyapps.io/wgbsExprs/ from files found here https://github.com/LieberInstitute/brain-epigenomics/tree/master/meth_vs_expr/meth_shiny with R 3.4.3. I'm now trying to update the deployed app using R 3.6.1 with some simple changes to the ui.R file (the citation information for the shiny app since it's tied to a paper that just got published 🎉) but it's breaking 😞with:

Clean code at deploy.R

> load('.deploy_info.Rdata')
> rsconnect::setAccountInfo(name=deploy_info$name, token=deploy_info$token,
+     secret=deploy_info$secret)
> rsconnect::deployApp(appFiles = c('ui.R', 'server.R', 'meth_df_withSymbol.Rdata',
+     'meth_data.Rdata', 'global.R',
+     'tf_data.Rdata', 'google-analytics.js', 'www/LICENSE.txt'),
+     appName = 'wgbsExprs', account = 'jhubiostatistics', server = 'shinyapps.io')
Preparing to deploy application...Update application currently deployed at
https://jhubiostatistics.shinyapps.io/wgbsExprs/? [Y/n] Y
DONE
Uploading bundle for application: 302754...--- Please select a CRAN mirror for use in this session ---
DONE
Deploying bundle: 2448146 for application: 302754 ...
Waiting for task: 652014864
  building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 652014866 failed: Error parsing manifest: Unable to determine package source for Bioconductor package GenomicAlignments: Repository must be specified
> traceback()
3: stop(status$error, call. = FALSE)
2: client$waitForTask(taskId, quiet)
1: rsconnect::deployApp(appFiles = c("ui.R", "server.R", "meth_df_withSymbol.Rdata",
       "meth_data.Rdata", "global.R", "tf_data.Rdata", "google-analytics.js",
       "www/LICENSE.txt"), appName = "wgbsExprs", account = "jhubiostatistics",
       server = "shinyapps.io")

From the error message, https://github.com/rstudio/rsconnect/issues/372 and https://github.com/rstudio/rsconnect/issues/88 might be related. In particular, due to https://github.com/rstudio/rsconnect/issues/88 I re-installed GenomicAlignments using BiocManager::install('GenomicAlignments'). Though this makes me think that rsconnect might have issues with Bioconductor packages in general and the time frame is consistent with the change in how Bioconductor packages are installed (biocLite('pkg') was the norm for years, vs BiocManager::install('pkg') used now) and might be related to https://github.com/rstudio/rsconnect/issues/274. Reading https://github.com/rstudio/rsconnect/issues/372 prompted me to comment out options(repos = c(CRAN = "https://cran.rstudio.com")) in my ~/.Rprofile file, but it had no effect. I also tried using the latest rsconnect from GitHub but that failed too (on the repositories prompt, I select the cloud one at the top of the list). Furthermore, using RSwitch I went back to my R 3.4.4 installation (not 3.4.3 like the version that is currently deployed; I don't have that anymore) and tried from there, but I first had to update my rsconnect given the following error:

> rsconnect::setAccountInfo(name=deploy_info$name, token=deploy_info$token,
+     secret=deploy_info$secret)
Error: HTTP 426
GET https://api.shinyapps.io/v1/users/current/
The rsconnect package is out of date.
 Please update to the latest available on CRAN.

and then ran into the same initial error I see on R 3.6.1:

> rsconnect::deployApp(appFiles = c('ui.R', 'server.R', 'meth_df_withSymbol.Rdata',
+     'meth_data.Rdata', 'global.R',
+     'tf_data.Rdata', 'google-analytics.js', 'www/LICENSE.txt'),
+     appName = 'wgbsExprs', account = 'jhubiostatistics', server = 'shinyapps.io')
Preparing to deploy application...Update application currently deployed at
https://jhubiostatistics.shinyapps.io/wgbsExprs/? [Y/n] Y
DONE
Uploading bundle for application: 302754...DONE
Deploying bundle: 2448133 for application: 302754 ...
Waiting for task: 652013408
  building: Processing bundle: 2448133
  building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 652013409 failed: Error parsing manifest: Unable to determine package source for Bioconductor package GenomicAlignments: Repository must be specified

Sooo.... I'm not sure how to proceed here. This is using a Pro ShinyApps account from the JHU Biostatistics Department if that matters at all. Though I doubt it does based on the other issues I linked to.

If it's relevant, note that using shiny::runApp() works well in R 3.6.1.

If you need any other information, please let me know.

Best, Leo

R session info

Currently deployed (2019-09-26)

The documentation tab of https://jhubiostatistics.shinyapps.io/wgbsExprs/ prints the sesion information, which I see is:

setting  value                       
 version  R version 3.4.3 (2017-11-30)
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       Etc/UTC                     
 date     2019-09-26                  

 package              * version   date       source        
 AnnotationDbi          1.40.0    2017-12-20 Bioconductor  
 assertthat             0.2.0     2017-04-11 CRAN (R 3.4.3)
 base                 * 3.4.3     2017-12-01 local         
 Biobase              * 2.38.0    2017-12-12 Bioconductor  
 BiocGenerics         * 0.24.0    2017-12-07 Bioconductor  
 BiocParallel           1.12.0    2018-02-24 Bioconductor  
 biomaRt                2.34.2    2018-01-25 Bioconductor  
 Biostrings           * 2.46.0    2017-12-12 Bioconductor  
 bit                    1.1-12    2014-04-09 CRAN (R 3.4.3)
 bit64                  0.9-7     2017-05-08 CRAN (R 3.4.3)
 bitops                 1.0-6     2013-08-17 CRAN (R 3.4.3)
 blob                   1.1.0     2017-06-17 CRAN (R 3.4.3)
 bsseq                * 1.14.0    2018-03-19 Bioconductor  
 colorspace             1.3-2     2016-12-14 CRAN (R 3.4.3)
 compiler               3.4.3     2017-12-01 local         
 crosstalk              1.0.0     2016-12-21 CRAN (R 3.4.3)
 data.table             1.10.4-3  2017-10-27 CRAN (R 3.4.3)
 datasets             * 3.4.3     2017-12-01 local         
 DBI                    0.8       2018-03-02 CRAN (R 3.4.3)
 DelayedArray         * 0.4.1     2017-12-12 Bioconductor  
 devtools             * 1.13.5    2018-02-18 CRAN (R 3.4.3)
 digest                 0.6.15    2018-01-28 CRAN (R 3.4.3)
 DT                   * 0.4       2018-01-30 CRAN (R 3.4.3)
 GenomeInfoDb         * 1.14.0    2017-12-12 Bioconductor  
 GenomeInfoDbData       1.0.0     2017-12-20 Bioconductor  
 GenomicAlignments      1.14.1    2018-03-08 Bioconductor  
 GenomicFeatures        1.30.3    2018-02-13 Bioconductor  
 GenomicRanges        * 1.30.3    2018-03-08 Bioconductor  
 graphics             * 3.4.3     2017-12-01 local         
 grDevices            * 3.4.3     2017-12-01 local         
 grid                   3.4.3     2017-12-01 local         
 gtools                 3.5.0     2015-05-29 CRAN (R 3.4.3)
 htmltools              0.3.6     2017-04-28 CRAN (R 3.4.3)
 htmlwidgets            1.0       2018-01-20 CRAN (R 3.4.3)
 httpuv                 1.3.6.2   2018-03-02 CRAN (R 3.4.3)
 httr                   1.3.1     2017-08-20 CRAN (R 3.4.3)
 igraph                 1.1.2     2017-07-21 CRAN (R 3.4.3)
 IRanges              * 2.12.0    2017-12-12 Bioconductor  
 jsonlite               1.5       2017-06-01 CRAN (R 3.4.3)
 lattice                0.20-35   2017-03-25 CRAN (R 3.4.3)
 limma                  3.34.9    2018-03-03 Bioconductor  
 locfit                 1.5-9.1   2013-04-20 CRAN (R 3.4.3)
 magrittr               1.5       2014-11-22 CRAN (R 3.4.3)
 Matrix                 1.2-12    2017-11-16 CRAN (R 3.4.3)
 matrixStats          * 0.53.1    2018-02-11 CRAN (R 3.4.3)
 memoise                1.1.0     2017-04-21 CRAN (R 3.4.3)
 methods              * 3.4.3     2017-12-01 local         
 mime                   0.5       2016-07-07 CRAN (R 3.4.3)
 munsell                0.4.3     2016-02-13 CRAN (R 3.4.3)
 parallel             * 3.4.3     2017-12-01 local         
 permute                0.9-4     2016-09-09 CRAN (R 3.4.3)
 pillar                 1.2.1     2018-02-27 CRAN (R 3.4.3)
 pkgconfig              2.0.1     2017-03-21 CRAN (R 3.4.3)
 plyr                   1.8.4     2016-06-08 CRAN (R 3.4.3)
 prettyunits            1.0.2     2015-07-13 CRAN (R 3.4.3)
 progress               1.1.2     2016-12-14 CRAN (R 3.4.3)
 R.methodsS3            1.7.1     2016-02-16 CRAN (R 3.4.3)
 R.oo                   1.21.0    2016-11-01 CRAN (R 3.4.3)
 R.utils                2.6.0     2017-11-05 CRAN (R 3.4.3)
 R6                     2.2.2     2017-06-17 CRAN (R 3.4.3)
 RColorBrewer         * 1.1-2     2014-12-07 CRAN (R 3.4.3)
 Rcpp                   0.12.15   2018-01-20 CRAN (R 3.4.3)
 RCurl                  1.95-4.10 2018-01-04 CRAN (R 3.4.3)
 rlang                  0.2.0     2018-02-20 CRAN (R 3.4.3)
 RMySQL                 0.10.14   2018-02-26 CRAN (R 3.4.3)
 Rsamtools            * 1.30.0    2018-03-08 Bioconductor  
 RSQLite                2.0       2017-06-19 CRAN (R 3.4.3)
 rtracklayer            1.38.3    2018-03-08 Bioconductor  
 RUnit                  0.4.31    2015-11-06 CRAN (R 3.4.3)
 S4Vectors            * 0.16.0    2017-12-12 Bioconductor  
 scales                 0.5.0     2017-08-24 CRAN (R 3.4.3)
 SGSeq                * 1.12.0    2018-03-19 Bioconductor  
 shiny                * 1.0.5     2017-08-23 CRAN (R 3.4.3)
 stats                * 3.4.3     2017-12-01 local         
 stats4               * 3.4.3     2017-12-01 local         
 stringi                1.1.6     2017-11-17 CRAN (R 3.4.3)
 stringr                1.3.0     2018-02-19 CRAN (R 3.4.3)
 SummarizedExperiment * 1.8.1     2017-12-22 Bioconductor  
 tibble                 1.4.2     2018-01-22 CRAN (R 3.4.3)
 tools                  3.4.3     2017-12-01 local         
 utils                * 3.4.3     2017-12-01 local         
 withr                  2.1.1     2017-12-19 CRAN (R 3.4.3)
 XML                    3.98-1.10 2018-02-19 CRAN (R 3.4.3)
 xtable                 1.8-2     2016-02-05 CRAN (R 3.4.3)
 XVector              * 0.18.0    2017-12-12 Bioconductor  
 yaml                   2.1.18    2018-03-08 CRAN (R 3.4.3)
 zlibbioc               1.24.0    2017-12-12 Bioconductor

I don't have the version number for rsconnect saved from the time that I deployed the app.

Current deploy attempt

This is the R session info after trying to deploy with rsconnect::deployApp() and then confirming that the app works with shiny::runApp().

─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.1 (2019-07-05)
 os       macOS Mojave 10.14.6        
 system   x86_64, darwin15.6.0        
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/New_York            
 date     2019-09-26                  

─ Packages ───────────────────────────────────────────────────────────────────
 package              * version   date       lib
 AnnotationDbi          1.46.1    2019-08-20 [1]
 askpass                1.1       2019-01-13 [1]
 assertthat             0.2.1     2019-03-21 [1]
 backports              1.1.4     2019-04-10 [1]
 Biobase              * 2.44.0    2019-05-02 [1]
 BiocGenerics         * 0.30.0    2019-05-02 [1]
 BiocManager            1.30.4    2018-11-13 [1]
 BiocParallel         * 1.18.1    2019-08-06 [1]
 biomaRt                2.40.4    2019-08-19 [1]
 Biostrings           * 2.52.0    2019-05-02 [1]
 bit                    1.1-14    2018-05-29 [1]
 bit64                  0.9-7     2017-05-08 [1]
 bitops                 1.0-6     2013-08-17 [1]
 blob                   1.2.0     2019-07-09 [1]
 BSgenome               1.52.0    2019-05-02 [1]
 bsseq                * 1.20.0    2019-05-02 [1]
 callr                  3.3.2     2019-09-22 [1]
 cli                    1.1.0     2019-03-19 [1]
 colorout             * 1.2-1     2019-05-07 [1]
 colorspace             1.4-1     2019-03-18 [1]
 crayon                 1.3.4     2017-09-16 [1]
 crosstalk              1.0.0     2016-12-21 [1]
 curl                   4.2       2019-09-24 [1]
 data.table             1.12.2    2019-04-07 [1]
 DBI                    1.0.0     2018-05-02 [1]
 DelayedArray         * 0.10.0    2019-05-02 [1]
 DelayedMatrixStats     1.6.1     2019-09-08 [1]
 desc                   1.2.0     2018-05-01 [1]
 devtools             * 2.2.1     2019-09-24 [1]
 digest                 0.6.21    2019-09-20 [1]
 DT                   * 0.9       2019-09-17 [1]
 ellipsis               0.3.0     2019-09-20 [1]
 fs                     1.3.1     2019-05-06 [1]
 GenomeInfoDb         * 1.20.0    2019-05-02 [1]
 GenomeInfoDbData       1.2.1     2019-04-10 [1]
 GenomicAlignments      1.20.1    2019-06-18 [1]
 GenomicFeatures        1.36.4    2019-07-09 [1]
 GenomicRanges        * 1.36.1    2019-09-06 [1]
 glue                   1.3.1     2019-03-12 [1]
 gtools                 3.8.1     2018-06-26 [1]
 HDF5Array              1.12.2    2019-08-06 [1]
 hms                    0.5.1     2019-08-23 [1]
 htmltools              0.3.6     2017-04-28 [1]
 htmlwidgets            1.3       2018-09-30 [1]
 httpuv                 1.5.2     2019-09-11 [1]
 httr                   1.4.1     2019-08-05 [1]
 igraph                 1.2.4.1   2019-04-22 [1]
 IRanges              * 2.18.3    2019-09-24 [1]
 jsonlite               1.6       2018-12-07 [1]
 later                  0.8.0     2019-02-11 [1]
 lattice                0.20-38   2018-11-04 [1]
 limma                  3.40.6    2019-07-26 [1]
 locfit                 1.5-9.1   2013-04-20 [1]
 magrittr               1.5       2014-11-22 [1]
 Matrix                 1.2-17    2019-03-22 [1]
 matrixStats          * 0.55.0    2019-09-07 [1]
 memoise                1.1.0     2017-04-21 [1]
 mime                   0.7       2019-06-11 [1]
 munsell                0.5.0     2018-06-12 [1]
 openssl                1.4.1     2019-07-18 [1]
 packrat                0.5.0     2018-11-14 [1]
 permute                0.9-5     2019-03-12 [1]
 pillar                 1.4.2     2019-06-29 [1]
 pkgbuild               1.0.5     2019-08-26 [1]
 pkgconfig              2.0.3     2019-09-22 [1]
 pkgload                1.0.2     2018-10-29 [1]
 prettyunits            1.0.2     2015-07-13 [1]
 processx               3.4.1     2019-07-18 [1]
 progress               1.2.2     2019-05-16 [1]
 promises               1.0.1     2018-04-13 [1]
 ps                     1.3.0     2018-12-21 [1]
 R.methodsS3            1.7.1     2016-02-16 [1]
 R.oo                   1.22.0    2018-04-22 [1]
 R.utils                2.9.0     2019-06-13 [1]
 R6                     2.4.0     2019-02-14 [1]
 RColorBrewer         * 1.1-2     2014-12-07 [1]
 Rcpp                   1.0.2     2019-07-25 [1]
 RCurl                  1.95-4.12 2019-03-04 [1]
 remotes                2.1.0     2019-06-24 [1]
 rhdf5                  2.28.0    2019-05-02 [1]
 Rhdf5lib               1.6.1     2019-09-09 [1]
 rlang                  0.4.0     2019-06-25 [1]
 rprojroot              1.3-2     2018-01-03 [1]
 Rsamtools            * 2.0.1     2019-09-19 [1]
 rsconnect            * 0.8.15    2019-07-22 [1]
 RSQLite                2.1.2     2019-07-24 [1]
 rtracklayer            1.44.4    2019-09-06 [1]
 RUnit                  0.4.32    2018-05-18 [1]
 S4Vectors            * 0.22.1    2019-09-09 [1]
 scales                 1.0.0     2018-08-09 [1]
 sessioninfo            1.1.1     2018-11-05 [1]
 SGSeq                * 1.18.0    2019-05-02 [1]
 shiny                * 1.3.2     2019-04-22 [1]
 stringi                1.4.3     2019-03-12 [1]
 stringr                1.4.0     2019-02-10 [1]
 SummarizedExperiment * 1.14.1    2019-07-31 [1]
 testthat             * 2.2.1     2019-07-25 [1]
 tibble                 2.1.3     2019-06-06 [1]
 usethis              * 1.5.1     2019-07-04 [1]
 vctrs                  0.2.0     2019-07-05 [1]
 withr                  2.1.2     2018-03-15 [1]
 XML                    3.98-1.20 2019-06-06 [1]
 xtable                 1.8-4     2019-04-21 [1]
 XVector              * 0.24.0    2019-05-02 [1]
 yaml                   2.2.0     2018-07-25 [1]
 zeallot                0.1.0     2018-01-28 [1]
 zlibbioc               1.30.0    2019-05-02 [1]
 source                            
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      
 Bioconductor                      
 CRAN (R 3.6.0)                    
 Bioconductor                      
 Bioconductor                      
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      
 Bioconductor                      
 CRAN (R 3.6.1)                    
 CRAN (R 3.6.0)                    
 Github (jalvesaq/colorout@7ea9440)
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.1)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.1)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      
 Bioconductor                      
 Bioconductor                      
 Bioconductor                      
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.1)                    
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.1)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.1)                    
 CRAN (R 3.6.1)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      
 CRAN (R 3.6.0)                    
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
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 Bioconductor                      
 CRAN (R 3.6.0)                    
 CRAN (R 3.6.0)                    
 Bioconductor                      

[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

Here's the R session information from my last deploy attempt using rsconnect's GitHub version instead of the CRAN one.

> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 3.6.1 (2019-07-05)
 os       macOS Mojave 10.14.6
 system   x86_64, darwin15.6.0
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2019-09-26

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version date       lib source
 askpass       1.1     2019-01-13 [1] CRAN (R 3.6.0)
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 3.6.0)
 backports     1.1.4   2019-04-10 [1] CRAN (R 3.6.0)
 BiocManager   1.30.4  2018-11-13 [1] CRAN (R 3.6.0)
 callr         3.3.2   2019-09-22 [1] CRAN (R 3.6.1)
 cli           1.1.0   2019-03-19 [1] CRAN (R 3.6.0)
 colorout    * 1.2-1   2019-05-07 [1] Github (jalvesaq/colorout@7ea9440)
 crayon        1.3.4   2017-09-16 [1] CRAN (R 3.6.0)
 curl          4.2     2019-09-24 [1] CRAN (R 3.6.1)
 desc          1.2.0   2018-05-01 [1] CRAN (R 3.6.0)
 devtools    * 2.2.1   2019-09-24 [1] CRAN (R 3.6.1)
 digest        0.6.21  2019-09-20 [1] CRAN (R 3.6.0)
 ellipsis      0.3.0   2019-09-20 [1] CRAN (R 3.6.0)
 fs            1.3.1   2019-05-06 [1] CRAN (R 3.6.0)
 glue          1.3.1   2019-03-12 [1] CRAN (R 3.6.0)
 jsonlite      1.6     2018-12-07 [1] CRAN (R 3.6.0)
 magrittr      1.5     2014-11-22 [1] CRAN (R 3.6.0)
 memoise       1.1.0   2017-04-21 [1] CRAN (R 3.6.0)
 openssl       1.4.1   2019-07-18 [1] CRAN (R 3.6.0)
 packrat       0.5.0   2018-11-14 [1] CRAN (R 3.6.0)
 pkgbuild      1.0.5   2019-08-26 [1] CRAN (R 3.6.1)
 pkgload       1.0.2   2018-10-29 [1] CRAN (R 3.6.0)
 prettyunits   1.0.2   2015-07-13 [1] CRAN (R 3.6.0)
 processx      3.4.1   2019-07-18 [1] CRAN (R 3.6.0)
 ps            1.3.0   2018-12-21 [1] CRAN (R 3.6.0)
 R6            2.4.0   2019-02-14 [1] CRAN (R 3.6.0)
 Rcpp          1.0.2   2019-07-25 [1] CRAN (R 3.6.0)
 remotes       2.1.0   2019-06-24 [1] CRAN (R 3.6.0)
 rlang         0.4.0   2019-06-25 [1] CRAN (R 3.6.0)
 rprojroot     1.3-2   2018-01-03 [1] CRAN (R 3.6.0)
 rsconnect     0.8.15  2019-09-26 [1] Github (rstudio/rsconnect@2a5b11b)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.6.0)
 testthat    * 2.2.1   2019-07-25 [1] CRAN (R 3.6.0)
 usethis     * 1.5.1   2019-07-04 [1] CRAN (R 3.6.0)
 withr         2.1.2   2018-03-15 [1] CRAN (R 3.6.0)

[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

Finally, here's the R session information from my attempt with R 3.4.4 and a new rsconnect:

> library('rsconnect')

Attaching package: ‘rsconnect’

The following object is masked from ‘package:devtools’:

    lint

> load('.deploy_info.Rdata')
> rsconnect::setAccountInfo(name=deploy_info$name, token=deploy_info$token,
+     secret=deploy_info$secret)
> rsconnect::deployApp(appFiles = c('ui.R', 'server.R', 'meth_df_withSymbol.Rdata',
+     'meth_data.Rdata', 'global.R',
+     'tf_data.Rdata', 'google-analytics.js', 'www/LICENSE.txt'),
+     appName = 'wgbsExprs', account = 'jhubiostatistics', server = 'shinyapps.io')
Preparing to deploy application...Update application currently deployed at
https://jhubiostatistics.shinyapps.io/wgbsExprs/? [Y/n] Y
DONE
Uploading bundle for application: 302754...--- Please select a CRAN mirror for use in this session ---
DONE
Deploying bundle: 2448217 for application: 302754 ...
Waiting for task: 652026525
  building: Processing bundle: 2448217
  building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 652026526 failed: Error parsing manifest: Unable to determine package source for Bioconductor package GenomicAlignments: Repository must be specified
> traceback()
3: stop(status$error, call. = FALSE)
2: client$waitForTask(taskId, quiet)
1: rsconnect::deployApp(appFiles = c("ui.R", "server.R", "meth_df_withSymbol.Rdata",
       "meth_data.Rdata", "global.R", "tf_data.Rdata", "google-analytics.js",
       "www/LICENSE.txt"), appName = "wgbsExprs", account = "jhubiostatistics",
       server = "shinyapps.io")
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 3.4.4 Patched (2018-03-19 r74624)
 os       macOS  10.14.6
 system   x86_64, darwin15.6.0
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 tz       America/New_York
 date     2019-09-26

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package       * version date       source
 BiocInstaller   1.28.0  2017-10-31 Bioconductor
 clisymbols      1.2.0   2017-05-21 CRAN (R 3.4.0)
 colorout      * 1.2-0   2018-05-03 Github (jalvesaq/colorout@c42088d)
 curl            3.2     2018-03-28 CRAN (R 3.4.4)
 devtools      * 1.13.6  2018-06-27 cran (@1.13.6)
 digest          0.6.18  2018-10-10 cran (@0.6.18)
 jsonlite        1.5     2017-06-01 CRAN (R 3.4.0)
 magrittr        1.5     2014-11-22 cran (@1.5)
 memoise         1.1.0   2017-04-21 CRAN (R 3.4.0)
 openssl         1.0.1   2018-03-03 CRAN (R 3.4.3)
 packrat         0.4.9-2 2018-04-20 CRAN (R 3.4.4)
 R6              2.3.0   2018-10-04 cran (@2.3.0)
 rlang           0.3.0.1 2018-10-25 cran (@0.3.0.1)
 rsconnect     * 0.8.15  2019-07-22 CRAN (R 3.4.4)
 sessioninfo     1.0.0   2017-06-21 CRAN (R 3.4.1)
 testthat      * 2.0.0   2017-12-13 CRAN (R 3.4.3)
 withr           2.1.2   2018-03-15 CRAN (R 3.4.4)
tamburinif commented 5 years ago

Was having a similar error message and options(repos = BiocManager::repositories()) fixed it for me, maybe try that?

lcolladotor commented 5 years ago

Awesome @tamburinif! Your solution worked ^^ 🎉🎉